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Non-Canonical Peptides

Converting charmm parameter files (.par)

Submitted by ajasja on Mon, 2014-09-29 07:19
Category: 
Scoring
Non-Canonical Peptides

Is there perhaps a (python) script lying around somewhere in the src distribution to convert charmm parameter files (.prm) into mm_torsion_params.txt and mm_atom_properties.txt (in the database directory database\chemical\mm_atom_type_sets\fa_standard)?
I have added the MM parameters for R1A and now I naturally have a lot of missing types for the mm_* score terms. I’m thinking the easiest way to sort this out is just to regenerate the mm_torsion_params.txt and mm_atom_properties.txt from my working charmm parameter files?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Getting chi rotamers

Submitted by ajasja on Tue, 2014-08-26 12:11
Category: 
Non-Canonical Peptides
PyRosetta

Hi!

Is there a way to get rotamers in PyRosetta? I googled around and found this old post, but the conclusion seemed to be, that it might be easier to implement the parsing of the rotamer libraries again. Is this still the case?

I tried to explore on my own (see ipython notebook), but the most promising function

pose.residue(6).chi_rotamers(1)

returns

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Unsolved
Forums: 
PyRosetta - General

Problems when inserting spin-label R1A

Submitted by ajasja on Fri, 2014-06-27 04:14
Category: 
Non-Canonical Peptides
PyRosetta

Dear all,

I would like to use the spin-lable R1A (implemented as part of Rosetta EPR).
In database/chemical/residue_type_sets/fa_standard/residue_types.txt I activated the needed lines

## Spin label types
# kills my unit tests???
residue_types/spin_labels/R1A.params

Although the “kills my unit tests???” comment is not very encouraging:=)

The problem is:

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Unsolved
Forums: 
PyRosetta - General

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